Animal Paper Collection (Ongoing)

[2023.12.14] Here is a workshop involving animals and infants CV4Smalls Workshop! Feel free to check it out!

[2023.11.26] My own paper "MAMMAL" is published online in Nature Communications now!

[2023.06.10] The program of CV4Animals Workshop in CVPR 2023 is available!

[2022.08.08] Here is the Ph.D thesis of SEMIH GÜNEL (https://infoscience.epfl.ch/record/293821), who is the author of well-known DeepFly3D and LiftPose3D.

[2022.06.22] The 2nd CV4Animals Workshop in CVPR 2022 (https://www.cv4animals.com/) presents many excellent works on rodent 3D reconstruction!

[2022.01.02] To make it easy to track, I sort the papers using the timepoint I find them (not publication time), and add label badges to show paper features.

[2021.11.28] I recommend MMPose for 2D animal pose estimation. It has collected various kinds of datasets.

[2021.07.16] I recommend CV4Animal workshop in CVPR 2021 (https://www.cv4animals.com/) because it is a good collection of recent advances in animal pose estimation area!

Recently, markerless animal motion capture and 3D reconstruction attracts more and more attention in computer vision community. Inspired by remarkable techniques for markerless human motion capture, a few excellent literatures appear for animal modeling and reconstruction such as SMAL and DeepLabCut. However, there is still a long way before computer vision methods could capture natural motion of arbitary animals in industrial-grade.

Therefore, I contribute this repository to track every step towards the ultimate goal of high quality animal capture. If you want to add/remove an article, please send an email to Liang An(anliang at mail dot tsinghua dot edu dot cn). Thank all the authors for their contribution and support.

	Characterizing the structure of mouse behavior using Motion Sequencing Sherry Lin, Winthrop F. Gillis, Caleb Weinreb, Ayman Zeine, Samuel C. Jones, Emma M. Robinson, Jeffrey Markowitz, Sandeep Robert Datta In Nature Protocols 2024
	SUBTLE: An Unsupervised Platform with Temporal Link Embedding that Maps Animal Behavior Jea Kwon, Sunpil Kim, Dong-Kyum Kim, Jinhyeong Joo, SoHyung Kim, Meeyoung Cha, C. Justin Lee In IJCV 2024
	AWOL: Analysis WithOut synthesis using Language Silvia Zuffi, Michael J. Black In ECCV 2024
	Multi-view Tracking, Re-ID, and Social Network Analysis of a Flock of Visually Similar Birds in an Outdoor Aviary Shiting Xiao, Yufu Wang, Ammon Perkes, Bernd Pfrommer, Marc Schmidt, Kostas Daniilidis, Marc Badger In IJCV 2023
	DeepShapeKit: accurate 4D shape reconstruction of swimming fish Ruiheng Wu, Oliver Deussen, Liang Li In IROS 2022
	YOLO-Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos Alex Hoi Hang Chan, Prasetia Putra, Harald Schupp, Johanna Köchling, Jana Straßheim, Britta Renner, Julia Schroeder, William D. Pearse, Shinichi Nakagawa, Terry Burke, Michael Griesser, Andrea Meltzer, Saverio Lubrano, Fumihiro Kano In biorxiv 2024
	High-throughput unsupervised quantification of patterns in the natural behavior of marmosets William Menegas, Erin Corbett, Kimberly Beliard, Haoran Xu, Shivangi Parmar, Robert Desimone, Guoping Feng In biorxiv 2024
	Long-term tracking of social structure in groups of rats M´at´e Nagy, Jacob D. Davidson, G´abor V´as´arhelyi, D´aniel Abel, Enik˝o Kubinyi, Ahmed El Hady, Tam´as Vicsek In biorxiv 2024
	Marigold: A machine learning-based web app for zebrafish pose tracking Gregory Teicher, R. Madison Riffe, Wayne Barnaby, Gabrielle Martin, Benjamin E. Clayton, Josef G. Trapani, Gerald B. Downes In biorxiv 2024
	A Real-time Multi-Subject Three Dimensional Pose Tracking System for Analyzing Social Behaviors of Non-human Primates Chaoqun Cheng, Zijian Huang, Ruiming Zhang, Guozheng Huang, Han Wang, Likai Tang, Xiaoqin Wang In biorxiv 2024
	PriMAT: A robust multi-animal tracking model for primates in the wild Richard Vogg, Matthias Nuske, Marissa A. Weis, Timo L¨uddecke, Elif Karako¸c, Zurna Ahmed, Sofia M. Pereira, Suchinda Malaivijitnond, Suthirote Meesawat, Florentin W¨org¨otter, Peter M. Kappeler, Alexander Gail, Julia Ostner, Oliver Sch¨ulke, Claudia Fichtel, Alexander S. Ecker In biorxiv 2024
	Peering into the world of wild passerines with 3D-SOCS: synchronized video capture and posture estimation Michael Chimento, Alex Hoi Hang Chan, Lucy M. Aplin, Fumihiro Kano In biorxiv 2024
	Quantifying social roles in multi-animal videos using subject-aware deep-learning Kelly Goss, Lezio S. Bueno-Junior, Katherine Stangis, Théo Ardoin, Hanna Carmon, Jie Zhou, Rohan Satapathy, Isabelle Baker, Carolyn E. Jones-Tinsley, Miranda M. Lim, Brendon O. Watson, Cédric Sueur, Carrie R. Ferrario, Geoffrey G. Murphy, Bing Ye, Yujia Hu In biorxiv 2024
	Animal Avatars: Reconstructing Animatable 3D Animals from Casual Videos Remy Sabathier, Niloy J. Mitra, David Novotny In ECCV 2024
	Three-dimensional body reconstruction enables quantification of liquid consumption in small invertebrates Henrique Galante, Tomer J. Czaczkes, Massimo De Agrò In biorxiv 2024
	Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling and cloud-native open-source tools Dan Biderman, Matthew R. Whiteway, Cole Hurwitz, Nicholas Greenspan, Robert S. Lee, Ankit Vishnubhotla, Richard Warren, Federico Pedraja, Dillon Noone, Michael M. Schartner, Julia M. Huntenburg, Anup Khanal, Guido T. Meijer, Jean-Paul Noel, Alejandro Pan-Vazquez, Karolina Z. Socha, Anne E. Urai, The International Brain Laboratory, John P. Cunningham, Nathaniel B. Sawtell, Liam Paninski In Nature Methods 2024
	Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics Caleb Weinreb, Jonah E. Pearl, Sherry Lin, Mohammed Abdal Monium Osman, Libby Zhang, Sidharth Annapragada, Eli Conlin, Red Hoffmann, Sofia Makowska, Winthrop F. Gillis, Maya Jay, Ye Shaokai, Alexander Mathis, Mackenzie Weygandt Mathis, Talmo Pereira, Scott W. Linderman, Sandeep Robert Datta In Nature Methods 2024
	The Poses for Equine Research Dataset (PFERD) Ci Li, Ylva Mellbin, Johanna Krogager, Senya Polikovsky, Martin Holmberg, Nima Ghorbani, Michael J. Black, Hedvig Kjellström, Silvia Zuffi, Elin Hernlund In Scientific Data 2024
	VAREN: Very Accurate and Realistic Equine Network Silvia Zuffi, Ylva Mellbin, Ci Li, Markus Hoeschle, Hedvig Kjellström, Senya Polikovsky, Elin Hernlund, Michael J. Black In CVPR 2024
	TrAQ: a novel, versatile, semi-automated two-dimensional motor behavioural tracking software Davide Di Censo, Ilaria Rosa, Brigida Ranieri, Tiziana DiLorenzo, Marcello Alecci, Tiziana Marilena Florio, Angelo Galante In biorxiv 2024
	A 3Dwhole-face movement analysis system to uncover underlying physiology in mice Kyle Daruwalla, Irene Nozal Martin, Andrew Frankel, Diana Naglič, Zainab Ahmad, Xun Helen Hou In biorxiv 2024
	Deep Imputation for Skeleton Data (DISK) for Behavioral Science France Rose, Monika Michaluk, Timon Blindauer, Bogna M. Ignatowska-Jankowska, Liam O’Shaughnessy, Greg J. Stephens, Talmo D. Pereira, Marylka Y. Uusisaari, Katarzyna Bozek In biorxiv 2024
	Visuo-frontal interactions during social learning in freely moving macaques M. Franch, S. Yellapantula, A. Parajuli, N. Kharas, A. Wright, B. Aazhang, V. Dragoi In Nature 2024
	Neural signatures of natural behaviour in socializing macaques Camille Testard, Sébastien Tremblay, Felipe Parodi, Ron W. DiTullio, Arianna Acevedo-Ithier, Kristin L. Gardiner, Konrad Kording, Michael L. Platt In Nature 2024
	replicAnt: a pipeline for generating annotated images of animals in complex environments using Unreal Engine Fabian Plum, René Bulla, Hendrik K. Beck, Natalie Imirzian, David Labonte In Nature Communications 2023
	Investigating the use of odour and colour foraging cues by rosy-faced lovebirds (Agapornis roseicollis) using deep-learning based behavioural analysis Winson King Wai Tsang, Emily Shui Kei Poon, Chris Newman, Christina D. Buesching, Simon Yung Wa Sin In biorxiv 2024
	Automated 3D analysis of social head-gaze behaviors in freely moving marmosets Feng Xing, Alec G. Sheffield, Monika P. Jadi, Steve W.C Chang, Anirvan S. Nandy In biorxiv 2024
	A-SOiD, an active learning platform for expert-guided, data efficient discovery of behavior Jens F. Tillmann, Alexander I. Hsu, Martin K. Schwarz, Eric A. Yttri In Nature Methods 2024
	Anti-drift pose tracker (ADPT): A transformer-based network for robust animal pose estimation cross-species Guoling Tang, Yaning Han, Quanying Liu, Pengfei Wei In biorxiv 2024
	vmTracking: Virtual Markers Overcome Occlusion and Crowding in Multi-Animal Pose Tracking Hirotsugu Azechi, Susumu Takahashi In biorxiv 2024
	ARBUR, a machine learning-based analysis system for relating behaviors and ultrasonic vocalizations of rats Zhe Chen, Guanglu Jia, Qijie Zhou, Yulai Zhang, Zhenzhen Quan, Xuechao Chen, Toshio Fukuda, Qiang Huang, Qing Shi In biorxiv 2024
	WILDPOSE: A LONG-RANGE 3D WILDLIFE MOTION CAPTURE SYSTEM Naoya Muramatsu, Sangyun Shin, Qianyi Deng, Andrew Markham, Amir Patel In biorxiv 2024
	Combining Unity with machine vision to create low latency, flexible, and simple virtual realities Yuri Ogawa, Raymond Aoukar, Richard Leibbrandt, Jake S Manger, Zahra M Bagheri, Luke Turnbull, Chris Johnston, Pavan K Kaushik, Jan M Hemmi, Karin Nordström In biorxiv 2024
	MacAction: Realistic 3D macaque body animation based on multi-camera markerless motion capture Lucas M. Martini, Anna Bogn´ar, Rufin Vogels, Martin A. Giese In biorxiv 2024
	DAMM for the detection and tracking of multiple animals within complex social and environmental settings Gaurav Kaul, Jonathan McDevitt, Justin Johnson, Ada Eban-Rothschild In biorxiv 2024
	Computer Vision for Primate Behavior Analysis in the Wild Richard Vogg, Timo Luddecke, Jonathan Henrich, Sharmita Dey, Matthias Nuske, Valentin Hassler, Derek Murphy, Julia Fischer, Julia Ostner, Oliver Schulke, Peter M. Kappeler, Claudia Fichte, Alexander Gail, Stefan Treue, Hansjorg Scherberger, Florentin Worg otter, Alexander S. Ecker In arxiv 2024
	PanAf20K: A Large Video Dataset for Wild Ape Detection and Behaviour Recognition Otto Brookes et.al. In IJCV 2024
	Multi-animal 3D social pose estimation, identification and behaviour embedding with a few-shot learning framework Yaning Han, Ke Chen, Yunke Wang, Wenhao Liu, Zhouwei Wang, Xiaojing Wang, Chuanliang Han, Jiahui Liao, Kang Huang, Shengyuan Cai, Yiting Huang, Nan Wang, Jinxiu Li, Yangwangzi Song, Jing Li, Guodong Wang, Liping Wang, Yaping Zhang, Pengfei Wei In Nature Machine Intelligence 2024
	Facemap: a framework for modeling neural activity based on orofacial tracking Atika Syeda, Lin Zhong, Renee Tung, Will Long, Marius Pachitariu, Carsen Stringer In Nature Neuroscience 2023
	Three-dimensional surface motion capture of multiple freely moving pigs using MAMMAL Liang An, Jilong Ren, Tao Yu, Tang Hai, Yichang Jia, Yebin Liu In Nature Communications 2023
	DeepLabCut-based Behavioural and Posture Analysis in a Cricket Shota Hayakawa, Kosuke Kataoka, Masanobu Yamamoto, Toru Asahi, Takeshi Suzuki In biorxiv 2023
	Distinct developmental trajectories of autonomous behaviors and agency in rodents C Mitelut, M Diez Castro, RE Peterson, M Gonçalves, MM Gamer, SRO Nilsson, TD Pereira, DH Sanes In biorxiv 2023
	BARN: Behavior-Aware Relation Network for multi-label behavior detection in socially housed macaques Sen Yang, Zhi-Yuan Chen, Ke-Wei Liang, Cai-Jie Qin, Yang Yang, Wen-Xuan Fan, Chen-Lu Jie, Xi-Bo Ma In Zoological Research 2023
	CATER: Combined Animal Tracking & Environment Reconstruction Lars Haalck, Michael Mangan, Antoine Wystrach, Leo Clement, Barbara Webb, Benjamin Risse In Science Advances 2023
	SMART-BARN: Scalable multimodal arena for real-time tracking behavior of animals in large numbers Máté Nagy, Hemal Naik, Fumihiro Kano, Nora V. Carlson, Jens C. Koblitz, Martin Wikelski, Iain D. Couzin In Science Advances 2023
	Hierarchical organization of rhesus macaque behavior Benjamin Voloh, Benjamin R. Eisenreich, David J-N. Maisson, R. Becket Ebitz, Hyun Soo Park, Benjamin Y. Hayden, Jan Zimmermann In Oxford Open Neuroscience 2023
	Open-source tools for behavioral video analysis: Setup, methods, and best practices Kevin Luxem, Jennifer J Sun, Sean P Bradley, Keerthi Krishnan, Eric Yttri, Jan Zimmermann, Talmo D Pereira, Mark Laubach In Elife 2023
	Automated measurement of livestock body based on pose normalisation using statistical shape model Xinying Luo, Yihu Hu, Zicheng Gao, Hao Guo, Yang Su In Biosystems Engineering 2023
	Establishing an AI-based evaluation system that quantifies social/pathophysiological behaviors of common marmosets Takaaki Kaneko, Jumpei Matsumoto, Wanyi Lu, Xincheng Zhao, Louie Richard UenoNigh, Takao Oishi, Kei Kimura, Yukiko Otsuka, Andi Zheng, Kensuke Ikenaka, Kousuke Baba, Hideki Mochizuki, Hisao Nishijo, Ken-ichi Inoue, Masahiko Takada In biorxiv 2023
	Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress Joeri Bordes, Lucas Miranda, Maya Reinhardt, Sowmya Narayan, Jakob Hartmann, Emily L. Newman, Lea Maria Brix, Lotte van Doeselaar, Clara Engelhardt, Larissa Dillmann, Shiladitya Mitra, Kerry J. Ressler, Benno Pütz, Felix Agakov, Bertram Müller-Myhsok, Mathias V. Schmidt In Nature Communications 2023
	LoTE-Animal: A Long Time-span Dataset for Endangered Animal Behavior Understanding Dan Liu, Jin Hou, Shaoli Huang, Jing Liu, Yuxin He, Bochuan Zheng, Jifeng Ning, Jindong Zhang In ICCV 2023
	Stimulatory effect of monoacylglycerol lipase inhibitor MJN110 on locomotion and step kinematics demonstrated by high-precision 3D motion capture in mice Bogna M. Ignatowska-Jankowska, Aysen Gurkan Ozer, Alexander Kuck, Micah J. Niphakis, Daisuke Ogasawara, Benjamin F. Cravatt, Marylka Y. Uusisaari In biorxiv 2023
	NeuroMechFly 2.0, a framework for simulating embodied sensorimotor control in adult Drosophila Sibo Wang-Chen, Victor Alfred Stimpfling, Pembe Gizem Ozdil, Louise Genoud, Femke Hurtak, Pavan Ramdya In biorxiv 2023
	Simultaneous recording of ultrasonic vocalizations and sniffing from socially interacting individual rats using a miniature microphone Shanah Rachel John, Rishika Tiwari, Yizhaq Goussha, Rotem Amar, Alex Bizer, Shai Netser, Shlomo Wagner In biorxiv 2023
	Automated Maternal Behavior during Early life in Rodents (AMBER) pipeline Hannah E. Lapp, Melissa G. Salazar, Frances A. Champagne In biorxiv 2023
	Three-dimensional markerless motion capture of multiple freely behaving monkeys for automated characterization of social behavior Jumpei Matsumoto, Takaaki Kaneko, Kei Kimura, Salvador Blanco Negrete, Jia Guo, Naoko Suda-Hashimoto, Akihisa Kaneko, Mayumi Morimoto, Hiroshi Nishimaru, Tsuyoshi Setogawa, Yasuhiro Go, Tomohiro Shibata, Hisao Nishijo, Masahiko Takada, Ken-ichi Inoue In biorxiv 2023
	3D mouse pose from single‑view video and a new dataset Bo Hu, Bryan Seybold, Shan Yang, Avneesh Sud, Yi Liu, Karla Barron, Paulyn Cha, Marcelo Cosino, Ellie Karlsson, Janessa Kite, Ganesh Kolumam, Joseph Preciado, José Zavala‑Solorio, Chunlian Zhang, Xiaomeng Zhang, Martin Voorbach, Ann E.Tovcimak, J.Graham Ruby, David A. Ross In Scientific Reports 2023
	Animal3D: A Comprehensive Dataset of 3D Animal Pose and Shape Jiacong Xu, Yi Zhang, Jiawei Peng, Wufei Ma, Artur Jesslen, Pengliang Ji, Qixin Hu, Jiehua Zhang, Qihao Liu, Jiahao Wang, Wei Ji, Chen Wang, Xiaoding Yuan, Prakhar Kaushik, Guofeng Zhang, Jie Liu, Yushan Xie, Yawen Cui, Alan Yuille, Adam Kortylewski In ICCV 2023
	PPR: Physically Plausible Reconstruction from Monocular Videos Gengshan Yang, Shuo Yang, John Z. Zhang, Zachary Manchester, Deva Ramanan In ICCV 2023
	AmadeusGPT: a natural language interface for interactive animal behavioral analysis Shaokai Ye, Jessy Lauer, Mu Zhou, Alexander Mathis, Mackenzie Weygandt Mathis In NeurIPS 2023
	ARTIC3D: Learning Robust Articulated 3D Shapes from Noisy Web Image Collections Chun-Han Yao, Amit Raj, Wei-Chih Hung, Yuanzhen Li, Michael Rubinstein, Ming-Hsuan Yang, Varun Jampani In arxiv 2023
	Behavioral decomposition reveals rich encoding structure employed across neocortex in rats Bartul Mimica, Tuçe Tombaz, Claudia Battistin, Jingyi Guo Fuglstad, Benjamin A. Dunn, Jonathan R. Whitlock In Nature Communications 2023
	MABe22: A Multi-Species Multi-Task Benchmark for Learned Representations of Behavior Jennifer J. Sun, Markus Marks, Andrew W. Ulmer, Dipam Chakraborty, Brian Geuther, Edward Hayes, Heng Jia, Vivek Kumar, Sebastian Oleszko, Zachary Partridge, Milan Peelman, Alice Robie, Catherine E. Schretter, Keith Sheppard, Chao Sun, Param Uttarwar, Julian M. Wagner, Erik Werner, Joseph Parker, Pietro Perona, Yisong Yue, Kristin Branson, Ann Kennedy In ICML 2023
	3D-POP - An automated annotation approach to facilitate markerless 2D-3D tracking of freely moving birds with marker-based motion capture Hemal Naik, Alex Hoi Hang Chan, Junran Yang, Mathilde Delacoux, Iain D. Couzin, Fumihiro Kano, Mate Nagy In CVPR 2023
	SuperAnimal models pretrained for plug-and-play analysis of animal behavior Shaokai Ye, Anastasiia Filippova, Jessy Lauer, Maxime Vidal, Steffen Schneider, Tian Qiu, Alexander Mathis, Mackenzie Weygandt Mathis In arxiv 2023
	CatFLW: Cat Facial Landmarks in the Wild Dataset George Martvel, Nareed Farhat, Ilan Shimshoni, Anna Zamansky In CV4Animals Workshop in CVPR 2023
	Decompose to Generalize: Species-Generalized Animal Pose Estimation Guangrui Li, Yifan Sun, Zongxin Yang, Yi Yang In ICLR 2023
	MammalNet: A Large-scale Video Benchmark for Mammal Recognition and Behavior Understanding Jun Chen, Ming Hu, Darren J. Coker, Michael L. Berumen, Blair Costelloe, Sara Beery, Anna Rohrbach, Mohamed Elhoseiny In CVPR 2023
	BITE: Beyond Priors for Improved Three-D Dog Pose Estimation Nadine Rüegg, Shashank Tripathi, Konrad Schindler, Michael J. Black, Silvia Zuffi In CVPR 2023
	MagicPony: Learning Articulated 3D Animals in the Wild Shangzhe Wu, Ruining Li, Tomas Jakab, Christian Rupprecht, Andrea Vedaldi In CVPR 2023
	CLAMP: Prompt-based Contrastive Learning for Connecting Language and Animal Pose Xu Zhang, Wen Wang, Zhe Chen, Yufei Xu, Jing Zhang, Dacheng Tao In CVPR 2023
	3D shape reconstruction of semi-transparent worms Thomas P. Ilett, Omer Yuval, Thomas Ranner, Netta Cohen, David C. Hogg In CVPR 2023
	A robust and flexible deep-learning workflow for animal tracking Abhishek Dutta, Natalia Pérez-Campanero, Graham K. Taylor, Andrew Zisserman, Cait Newport In biorxiv 2023
	Analysis of antennal responses to motion stimuli in the honey bee by automated tracking using DeepLabCut Hiroki Kohno, Shuichi Kamata, Takeo Kubo In biorxiv 2023
	Learning Articulated Shape with Keypoint Pseudo-labels from Web Images Anastasis Stathopoulos, Georgios Pavlakos, Ligong Han, Dimitris Metaxas In CVPR 2023
	Farm3D: Learning Articulated 3D Animals by Distilling 2D Diffusion Tomas Jakab, Ruining Li, Shangzhe Wu, Christian Rupprecht, Andrea Vedaldi In arxiv 2023
	Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second Kevin C. Zhou, Mark Harfouche, Colin L. Cooke, Jaehee Park, Pavan C. Konda, Lucas Kreiss, Kanghyun Kim, Joakim Jönsson, Thomas Doman, Paul Reamey, Veton Saliu, Clare B. Cook, Maxwell Zheng, John P. Bechtel, Aurélien Bègue, Matthew McCarroll, Jennifer Bagwell, Gregor Horstmeyer, Michel Bagnat, Roarke Horstmeyer In Nature Photonics 2023
	Scalable Apparatus to Measure Posture and Locomotion (SAMPL): a high-throughput solution to study unconstrained vertical behavior in small animals Yunlu Zhu, Franziska Auer, Hannah Gelnaw, Samantha N. Davis, Kyla R. Hamling, Christina E. May, Hassan Ahamed, Niels Ringstad, Katherine I. Nagel, David Schoppik In biorxiv 2023
	ScarceNet: Animal Pose Estimation with Scarce Annotations Chen Li, Gim Hee Lee In CVPR 2023
	Lights, Camera, Mirrors, Action! Toolbox for 3D Analysis of High-rate Maneuvers Using a Single Camera and Planar Mirrors Wajahat Hussain, Mahum Naveed, Asad Khan, Taimoor Hasan Khan, Muhammad Latif Anjum, Shahzad Rasool, Adnan Maqsood In biorxiv 2023
	Unsupervised decomposition of natural monkey behavior into a sequence of motion motifs Koki Mimura, Jumpei Matsumoto, Daichi Mochihashi, Tomoaki Nakamura, Toshiyuki Hirabayashi, Makoto Higuchi, Takafumi Minamimoto In biorxiv 2023
	ArMo: An Articulated Mesh Approach for Mouse 3D Reconstruction James P. Bohnslav, Mohammed Abdal Monium Osman, Akshay Jaggi, Sofia Soares, Caleb Weinreb, Sandeep Robert Datta, Christopher D. Harvey In biorxiv 2023
	Predicting long-term collective animal behavior with deep learning Vaios Papaspyros, Ram´on Escobedo, Alexandre Alahi, Guy Theraulaz, Cl´ement Sire, Francesco Mondada In biorxiv 2023
	Three‑dimensional unsupervised probabilistic pose reconstruction (3D‑UPPER) for freely moving animals Aghileh S. Ebrahimi, Patrycja Orlowska‑Feuer, Qian Huang, AntonioG. Zippo, Franck P. Martial, Rasmus S. Petersen, Riccardo Storchi In Scientific Reports 2023
	A review of 28 free animal-tracking software applications: current features and limitations Veronica Panadeiro, Alvaro Rodriguez, Jason Henry, Donald Wlodkowic, Magnus Andersson In Lab Animal 2021
	JAX Animal Behavior System (JABS): A video-based phenotyping platform for the laboratory mouse Glen Beane, Brian Q. Geuther, Thomas J. Sproule, Anshul Choudhary, Jarek Trapszo, Leinani Hession, Vivek Kohar, Vivek Kumar In biorxiv 2023
	An 8-cage imaging system for automated analyses of mouse behavior Thaís Del Rosario Hernández, Narendra R. Joshi, Sayali V. Gore, Jill A. Kreiling, Robbert Creton In biorxiv 2023
	Quantifying the movement, behavior, and environmental context of group-living animals using drones and computer vision Benjamin Koger, Adwait Deshpande, Jeffrey T. Kerby, Jacob M. Graving, Blair R. Costelloe, Iain D. Couzin In Journal of Animal Ecology 2023
	Gait-level analysis of mouse open field behavior using deep learning-based pose estimation Keith Sheppard, Justin Gardin, Gautam Sabnis, Asaf Peer, Megan Darrell, Sean Deats, Brian Geuther, Cathleen M. Lutz, Vivek Kumar In Cell Reports 2022
	Markerless tracking of an entire honey bee colony Katarzyna Bozek, Laetitia Hebert, Yoann Portugal, Alexander S. Mikheyev, Greg J. Stephens In Nature Communications 2021
	Capturing the continuous complexity of behaviour in Caenorhabditis elegans Tosif Ahamed, Antonio C. Costa, Greg J. Stephens In Nature Physics 2020
	ConstrastivePose: A contrastive learning approach for self-supervised feature engineering for pose estimation and behavorial classification of interacting animals Tianxun Zhou, Calvin Chee Hoe Cheah, Eunice Wei Mun Chin, Jie Chen, Hui Jia Farm, Eyleen Lay Keow Goh, Keng Hwee Chiam In biorxiv 2022
	Common Pets in 3D: Dynamic New-View Synthesis of Real-Life Deformable Categories Samarth Sinha, Roman Shapovalov, Jeremy Reizenstein, Ignacio Rocco, Natalia Neverova, Andrea Vedaldi, David Novotny In arxiv 2022
	B-SOiD, an open-source unsupervised algorithm for identification and fast prediction of behaviors Alexander I. Hsu, Eric A. Yttri In Nature Communications 2022
	Estimation of skeletal kinematics in freely moving rodents Arne Monsees, Kay-Michael Voit, Damian J. Wallace, Juergen Sawinski, Edyta Charyasz, Klaus Scheffler, Jakob H. Macke, Jason N. D. Kerr In Nature Methods 2022
	OpenLabCluster: Active Learning Based Clustering and Classification of Animal Behaviors in Videos Based on Automatically Extracted Kinematic Body Keypoints Jingyuan Li, Moishe Keselman, Eli Shlizerman In biorxiv 2022
	LASSIE: Learning Articulated Shapes from Sparse Image Ensemble via 3D Part Discovery Chun-Han Yao, Wei-Chih Hung, Yuanzhen Li, Michael Rubinstein, Ming-Hsuan Yang, Varun Jampani In NeurIPS 2022
	Evaluation of mouse behavioral responses to nutritive versus nonnutritive sugar using a deep learning-based 3D real-time pose estimation system Jineun Kim, Dae-gun Kim, Wongyo Jung, Greg S. B. Suh In biorxiv 2022
	Development of a new 3D tracking system for multiple marmosets under free-moving conditions Terumi Yurimoto, Wakako Kumita, Kenya Sato, Rika Kikuchi, Yusuke Shibuki, Rino Hashimoto, Michiko Kamioka, Yumi Hayasegawa, Eiko Yamazaki, Yoko Kurotaki, Norio Goda, Junichi Kitakami, Tatsuya Fujita, Takashi Inoue, Erika Sasaki In biorxiv 2022
	LabGym: quantification of user-defined animal behaviors using learning-based holistic assessment Yujia Hu, Carrie R. Ferrario, Alexander D. Maitland, Rita B. Ionides, Anjesh Ghimire, Brendon Watson, Kenichi Iwasaki, Hope White, Yitao Xi, Jie Zhou, Bing Ye In Cell Reports Methods 2022
	BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking Christopher J Gabriel, Zachary Zeidler, Benita Jin, Changliang Guo, Caitlin M Goodpaster, Adrienne Q Kashay, Anna Wu, Molly Delaney, Jovian Cheung, Lauren E DiFazio, Melissa J Sharpe, Daniel Aharoni, Scott A Wilke, Laura A DeNardo In eLife 2022
	Cross-Skeleton Interaction Graph Aggregation Network for Representation Learning of Mouse Social Behaviour Feixiang Zhou, Xinyu Yang, Fang Chen, Long Chen, Zheheng Jiang, Hui Zhu, Reiko Heckel, Haikuan Wang, Minrui Fei, Huiyu Zhou In arxiv 2022
	Animal pose estimation: A closer look at the state-of-the-art, existing gaps and opportunities Le Jiang, Caleb Lee, Divyang Teotia, Sarah Ostadabbas In Computer Vision and Image Understanding (CVIU) 2022
	3D pose estimation enables virtual head fixation in freely moving rats Artur Schneider, Christian Zimmermann, Mansour Alyahyay, Florian Steenbergen, Thomas Brox, Ilka Diester In Neuron 2022
	Natural behavior is the language of the brain Cory T. Miller, David Gire, Kim Hoke, Alexander C. Huk, Darcy Kelley, David A. Leopold, Matthew C. Smear, Frederic Theunissen, Michael Yartsev, Cristopher M. Niell In Current Biology 2022
	Deep-learning based identification, tracking, pose estimation, and behavior classification of interacting primates and mice in complex environments Markus Marks, Jin Qiuhan, Oliver Sturman, Lukas von Ziegler, Sepp Kollmorgen, Wolfger von der Behrens, Valerio Mante, Johannes Bohacek, Mehmet Fatih Yanik In Nature Machine Intelligence 2022
	EXPLORE: A novel deep learning-based analysis method for exploration behaviour in object recognition tests Victor Iba˜nez, Laurens Bohlen, Francesca Manuell, Isabelle Mansuy, Fritjof Helmchen, Anna-Sophia Wahl In biorxiv 2022
	TRex, a fast multi-animal tracking system with markerless identification, 2D body posture estimation and visual field reconstruction Tristan Walter, Iain D Couzin In eLife 2021
	Unsupervised behaviour analysis and magnification (uBAM) using deep learning Biagio Brattoli, Uta Büchler, Michael Dorkenwald, Philipp Reiser, Linard Filli, Fritjof Helmchen, Anna-Sophia Wahl, Björn Ommer In Nature Machine Intelligence 2021
	Leaving Flatland: Advances in 3D behavioral measurement Jesse D. Marshall, Tianqing Li, Joshua H. Wu, Timothy W. Dunn In Current Opinion in Neurobiology 2022
	Improved Markerless 3D Animal Pose Estimation Using Temporal Semi-Supervision Tianqing Li, Kyle S. Severson, Fan Wang, Timothy W. Dunn In CV4Animal workshop at CVPR 2022
	A whole-body musculoskeletal model of the mouse Shravan Tata Ramalingasetty, Simon M. Danner, Jonathan Arreguit, Sergey N. Markin, Dimitri Rodarie, Claudia Kathe, Grégoire Courtine, Ilya A. Rybak, Auke Ijspeert In IEEE Access 2021
	AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time Dae-Gun Kim, Anna Shin, Yong-Cheol Jeong, Seahyung Park, Daesoo Kim In biorxiv 2022
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	Deep Cross-species Feature Learning for Animal Face Recognition via Residual Interspecies Equivariant Network Xiao Shi, Chenxue Yang, Xue Xia, Xiujuan Chai In ECCV 2020
	RGBD-Dog: Predicting Canine Pose from RGBD Sensors Sinead Kearney, Wenbin Li, Martin Parsons, Kwang In Kim, Darren Cosker In CVPR 2020
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Last updated in Sep 2024

This repository is inspired by Cat Papers with some code borrowed from it. Paper and project signs are taken from http://kesen.realtimerendering.com/.